version 0.95alpha

1 files changed, 82 insertions, 0 deletions

diff --git a/src/vc.h b/src/vc.h
new file mode 100644
index 0000000..f34d72e
--- /dev/null
+++ b/src/vc.h
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+/*
+	Genome-wide Efficient Mixed Model Association (GEMMA)
+    Copyright (C) 2011  Xiang Zhou
+
+    This program is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+#ifndef __VC_H__                
+#define __VC_H__
+
+#include "gsl/gsl_vector.h"
+#include "gsl/gsl_matrix.h"
+
+
+#ifdef FORCE_FLOAT
+#include "param_float.h"
+#include "io_float.h"
+#else
+#include "param.h"
+#include "io.h"
+#endif
+
+using namespace std;
+
+
+
+class VC_PARAM
+{
+
+public:	
+	const gsl_matrix *K;
+	const gsl_matrix *W;
+	const gsl_vector *y;
+	gsl_matrix *P;
+	gsl_vector *Py;
+	gsl_matrix *KPy_mat;
+	gsl_matrix *PKPy_mat;
+	gsl_matrix *Hessian;
+};
+
+
+
+
+class VC {
+
+public:
+	// IO related parameters
+	string file_out;
+	string path_out;
+
+	vector<double> v_sigma2;
+	vector<double> v_se_sigma2;
+	vector<double> v_pve;
+	vector<double> v_se_pve;
+	vector<double> v_traceG;
+	vector<double> v_beta;
+	vector<double> v_se_beta;
+
+	double time_UtX;
+	double time_opt;
+	
+	// Main functions
+	void CopyFromParam (PARAM &cPar);
+	void CopyToParam (PARAM &cPar);
+	void CalcVChe (const gsl_matrix *K, const gsl_matrix *W, const gsl_vector *y);
+	void CalcVCreml (const gsl_matrix *K, const gsl_matrix *W, const gsl_vector *y);
+};
+
+#endif
+
+